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Extract values from the stream order .gpkg files.

Source: R/extract_from_gpkg.R
extract_from_gpkg.Rd

The function reads the attribute table of the stream network GeoPackage file (.gpkg) stored on disk and extracts the data for one or more (or all) input sub-catchment (i.e. stream segment) IDs. The output is a data.table, and only the output is loaded into R.

Usage

extract_from_gpkg(
  data_dir,
  subc_id,
  subc_layer,
  var_layer,
  out_dir = NULL,
  file_name = NULL,
  n_cores = NULL,
  quiet = TRUE
)

Arguments

data_dir

character. Path to the directory containing all input data.

subc_id

a numeric vector of sub-catchment IDs or "all". If "all", the attribute table is extracted for all the stream segments of the input .gpkg layer. The stream segment IDs are the same as the sub-catchment IDs. A vector of the sub-catchment IDs can be acquired from the extract_ids() function, by sub-setting the resulting data.frame.

subc_layer

character. Full path to the sub-catchment ID .tif layer

var_layer

character vector of .gpkg files on disk, e.g. "order_vect_point_h18v04.gpkg".

out_dir

character. The directory where the output will be stored. If the out_dir is specified, the attribute tables will be stored as .csv files in this location, named after their input variable vector files (e.g. "/path/to/stats_order_vect_point_h18v04.csv"). If NULL, the output is only loaded in R and not stored on disk.

file_name

character. Name of the .csv file where the output table will be stored. out_dir should also be specified for this purpose.

n_cores

numeric. Number of cores used for parallelization, in case multiple .gpkg files are provided to var_layer. If NULL, available cores - 1 will be used.

quiet

logical. If FALSE, the standard output will be printed. Default is TRUE.

Details

The following attributes are stored in the stream network .gpkg files (as produced by the GRASS GIS function r.stream.order:

  • cat - category

  • stream - sub-catchment / stream segment ID (equal to cat)

  • next_stream - downstream sub-catchment / stream segment ID

  • prev_streams; two or more uptstream sub-catchment / stream segment IDs

  • strahler - Strahler's stream order

  • horton - Hortons's stream order

  • shreve - Shreve's stream magnitude

  • hack - Hack's main streams or Gravelius order

  • topo_dim - Topological dimension streams order

  • scheidegger - Scheidegger's Consisted Associated Integers

  • drwal - Drwal's stream hierarchy

  • length - length of the stream segment

  • stright - length of the stream segment as a stright line

  • sinusoid - fractal dimension: stream segment length / stright stream

  • segment length;

  • cum_length - length of the stream from the source

  • flow_accum - flow accumulation within the sub-catchment of a stream segment

  • out_dist - distance of current stream initialisation from outlet

  • source_elev - elevation at stream segment initialisation

  • outlet_elev - elevation at stream segment outlet

  • elev_drop difference between source_elev and outlet_elev + drop outlet

  • out_drop - drop at the outlet of the stream segment

  • gradient - drop/length

References

https://grass.osgeo.org/grass82/manuals/v.in.ogr.html https://grass.osgeo.org/grass82/manuals/addons/r.stream.order.html

Author

Afroditi Grigoropoulou, Jaime Garcia Marquez, Marlene Schürz

Examples

# Download test data into temporary R folder
# or define a different directory
my_directory <- tempdir()
download_test_data(my_directory)

# Define path to the directory containing all input data
test_data <- paste0(my_directory, "/hydrography90m_test_data")

# Define sub-catchment ID layer
subc_raster <- paste0(my_directory, "/hydrography90m_test_data",
                  "/subcatchment_1264942.tif")

# Extract the attribute table of the file order_vect_59.gpkg for all the
# sub-catchment IDs of the subcatchment_1264942.tif raster layer
attribute_table <- extract_from_gpkg(data_dir = test_data,
                                     subc_id = "all",
                                     subc_layer = subc_raster,
                                     var_layer = "order_vect_59.gpkg",
                                     n_cores = 1)

# Show the output table
attribute_table